WASHINGTONA federal agent who launched the investigation that ultimately led to the resignation of Central Intelligence Agency chief David Petraeus was barred from taking part in the case over the summer due to superiors' concerns that he was personally involved in the case, according to officials familiar with the probe.

After being blocked from the case, the agent continued to press the matter, relaying his concerns to a member of Congress, the officials said.

New details about how the Federal Bureau of Investigation handled the case suggest that even as the bureau delved into Mr. Petraeus's personal life, the agency had to address conduct by its own agentwho allegedly sent shirtless photos of himself to a woman involved in the case prior to the investigation.

The FBI agent who started the case was a friend of Jill Kelley, the Tampa woman who received harassing, anonymous emails that led to the probe, according to officials. Ms. Kelley, a volunteer who organizes social events for military personnel in the Tampa area, complained in May about the emails to a friend who is an FBI agent. That agent referred it to a cyber crimes unit, which opened an investigation.

However, supervisors soon became concerned that the initial agent might have grown obsessed with the matter, and prohibited him from any role in the investigation, according to the officials.

(CNN) -- The spiraling scandal that took down David Petraeus has apparently ensnared another powerful general, as authorities announced that Gen. John Allen is under investigation for allegedly sending inappropriate messages to Jill Kelley, a woman who has been linked to the Petraeus scandal.

Allen, who is the commander of NATO's International Security Assistance Force, has denied any wrongdoing, a senior defense official said.

Details of the latest angle of the scandal that has shaken the highest level of the military were sketchy early Tuesday morning.

Just like Uncle Ferd says - dem womens'll mess ya up ever' time...Top U.S. commander in Afghanistan under investigationNovember 13th, 2012 - The spiraling scandal that took down David Petraeus has apparently claimed another powerful general, as authorities announced that Gen. John Allen is under investigation for allegedly sending inappropriate messages to Jill Kelley, a woman who has been linked to the Petraeus scandal.

Allen, who is the commander of NATO's International Security Assistance Force, has disputed that he has committed any wrongdoing, a senior defense official said. Details of the latest angle of the scandal that has shaken the highest level of the military were sketchy early Tuesday morning. Some details about Allen, the top U.S. commander in Afghanistan, came from a terse overnight statement by Defense Secretary Leon Panetta. "On Sunday, the Federal Bureau of Investigation referred to the Department of Defense a matter involving General John Allen, Commander of the International Security Assistance Force (or ISAF) in Afghanistan," part of the statement said. "Today, the secretary directed that the matter be referred to the Inspector General of the Department of Defense for investigation."

A defense official told CNN that there is a"distinct possibility" that the investigation into Allen is connected to the investigation that led to the resignation of Petraeus. Allen will still retain his position as the commander of ISAF as the investigation continues, the Pentagon said. But Panetta asked that Allen's nomination to become NATO's supreme allied commander be put on hold, the statement said.

The confirmation hearing to see if Allen would get that lofty military post was scheduled for Thursday. The investigation was in its early stages but authorities were looking into some 20,000 to 30,000 pages of documents, the defense official said.

Analysis: Will national security scandal create national security risk?November 13th, 2012 - The fallout from the scandal involving now disgraced CIA Director Gen. David Petraeus and possible connection to top Afghan commander Gen. John Allen comes at a transition time for the Obama administration. Just a week after the election, one of Washington's favorite guessing games started as politicians, journalists and every other political wonk started to calculate who could be filling the major Cabinet positions that would be opening as some get set to step down. It raises the question of what effect all this could have on the country's national security.

Secretary of State Hillary Clinton long ago announced she would be leaving and Secretary of Defense Leon Panetta, said this week that he does want to return to his home in California. Asked how long he plans to stick around the Pentagon, he responded to reporters, "Who the hell knows?" In the military, regularly scheduled command changes were getting set as well, as Allen was moving to head the European Command and a new commander was preparing to take over in Afghanistan. Both have to be confirmed by the Senate and a confirmation hearing is set for Thursday with the Senate Armed Services Committee. But in light of the scandal, is the president at risk of losing too much of his foreign policy brain trust as Petraeus departs and Allen works under the haze of an investigation?

White House spokesman Jay Carney addressed that question Tuesday, saying the president, "has great confidence in the acting CIA director. He has confidence in his military, and the secretary of Defense and the Defense Department to carry out the missions that he has assigned to them." Mark Jacobson, a former NATO adviser to Petraeus while he was in Afghanistan and now a fellow at the policy analysis group The German Marshall Fund, says a scandal like this would not affect national security. "What it is, is a loss for the CIA, which does need some restructuring, as does the Pentagon, Defense Intelligence Agency and the National Security Agency. Folks need to move away from Afghanistan and Iraq and start looking at the long-term strategic picture and I think Petraeus was the right guy to do that for the agency," Jacobson said. "There was a thought he (Petraeus) could be leaving to head up Princeton this year, so he might have left anyhow," Jacobson said.

But if the personal nature of the relationship between Petraeus and his biographer, Paula Broadwell, does not have a consequence on national security, surely the decision-making process of who will fill the open positions could have a trickle down effect. For instance, if the Obama administration loses its top CIA boss and its top commander in Afghanistan, on top of the departure of Clinton and the expected departure of Panetta, who could possibly oversee the sensitive diplomatic and military mission of the final two years of U.S. troops in Afghanistan?

Surprisingly, many in Washington think there are plenty of qualified people who can fill these gaps. In fact, many national security staffers on Capitol Hill we spoke with Tuesday believe the scandal will not hollow out those with national security experience in the administration. "It's not like there is a void of qualified people. If that was the case the president would have to keep Petraeus in his job," said one Capitol Hill staffer who asked not to be identified. But one senior Hill staffer thinks the Pentagon's decision to not outright fire Allen and keep him in his position is not only a signal that the military does not know if he was in the wrong, but also a way to protect him if he is found not to be at fault. "It would be a shame to lose a man with the experience he has in Afghanistan if they were to fire him only to find that he was not actually guilty of anything," the staffer said.

one important political factor has emerged in the last day: Republican House Majority Leader Eric Cantor appears to have tried to put pressure on the FBI to advance the investigation, with the likely goal of an October surprise scandal that would have potentially harmed Obama's chance of re-election.

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Cantor's inappropriate meddling into an FBI investigation for opportunistic political purposes -- likely aimed at influencing an election -- simply failed. Cantor took the risk of assisting a rogue FBI agent to make an end run around his superiors, without even informing his fellow Republicans on the Hill. He thought he would end up a GOP hero, but he really just looks as seedy as the whole lamentable saga.

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